Help with open_basedir

I am having to rebuild my server manually and I came across an issue. all my Code Igniter sites are receiving an open_basedir error. The sites have the application and system directories set as siblings under the parent web? directory. i.e.:

I am receiving the following error: Message: is_file(): open_basedir restriction in effect.
File(application/modules/index.html/config/routes.php) is not within the allowed path(s): (/var/www/clients/client1/web1/web:/var/www/clients/client1/web1/tmp:/var/www/[CUT-SITENAME]/web:/srv/www/[CUT-SITENAME]/web:/usr/share/php5:/tmp:/usr/share/phpmyadmin:/etc/phpmyadmin:/var/lib/phpmyadmin:/usr/share/php)

Filename: MX/Modules.php

Line Number: 369

I have the following line in the PHP open_basedir option: /var/www/clients/client1/web1/web:/var/www/clients/client1/web1/tmp:/var/www/[CUT-SITENAME]/web:/srv/www/[CUT - SITENAME]/web:/usr/share/php5:/tmp:/usr/share/phpmyadmin:/etc/phpmyadmin:/var/lib/phpmyadmin:/usr/share/php